title: ENVIRONMENTAL STRESSORS IMPACT PLACENTATION THROUGH ACTIONS ON TROPHOBLAST, IMMUNE , AND ENDOTHELIAL CELL DYNAMICS [RNA-Seq]

status: Public on Nov 30 2021

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

country: USA

institute: University of Kansas Medical Center

type: Expression profiling by high throughput sequencing

summary: Our environment is replete with chemicals that can affect embryonic and extraembryonic development.  Dioxins, such as 2,3,7,8-tetrachlorodibenzodioxin (TCDD), are compounds affecting development through the aryl hydrocarbon receptor (AHR). TCDD exposures can lead to placental adaptations and at higher doses pregnancy termination.  Deep intrauterine endovascular trophoblast cell invasion was a prominent placentation site adaptation to TCDD. TCDD-mediated placental adaptations were dependent upon maternal AHR signaling but not placental or fetal AHR nor the presence of a prominent AHR target, cytochrome P450 1A1 (CYP1A1).  At the placentation site, TCDD stimulated CYP1A1 transcription within endothelial cells but not trophoblast cells.  Immune and trophoblast cell behaviors at the uterine-placental interface were guided by the actions of TCDD on endothelial cells.  In summary, we have identified an AHR regulatory pathway activated by environmental stressors affecting uterine and trophoblast cell dynamics and the formation of the hemochorial placenta.

overall_design: Pregnant rats treaatted with TCDD at gestational day (gd) 6.5 and placental-uterine inerface tissue was collected at gd 13.5.

first: Michael

middle: J

last: Soares


title: LncRNA Uc003xsl.1 Activates of NF-κB/IL8 Axis to Promotes Triple-negative Breast Cancer Progression via A Decoy Role to NKRF [lnc231]

status: Public on Nov 29 2021

city: chengdu

first: huang

last: liang

address: No.24, South First Section, First Ring Road, Wuhou District, Chengdu City

country: China

institute: sicuan university

type: Non-coding RNA profiling by high throughput sequencing

summary: To discover the potential drivers of TNBC metastasis, we established an in vivo model by injecting MDA-MB-231cells into the tail veins of mice. Then, the breast tumor cells that successfully grew into metastatic lung tumors were collected and expanded in vitro, followed by re-injected into the tail veins of mice for lung metastasis. After three rounds of selection, a highly metastatic subline, MDA-MB-231-P3, was established, and more frequent micro-metastasis was detected in MDA-MB-231-P3 groups than that of MDA-MB-231 groups when the lungs of mice were stained with hematoxylin and eosin (HE). The lncRNA profiles of MDA-MB-231 or MDA-MB-231-P3 cells were analyzed by lncRNA sequencing. A total of 267 lncRNAs in MDA-MB-231-P3 cells were upregulated more than 2-fold in comparison to the MDA-MB-231 cells.

first: Ying

last: Xu

first: Qingjian

last: Li

first: Chaohui

last: Duan

first: Herui

last: Yao


title: LncRNA Uc003xsl.1 Activates of NF-κB/IL8 Axis to Promotes Triple-negative Breast Cancer Progression via A Decoy Role to NKRF [lnc_p]

summary: To identify which of these lncRNAs were specifically involved in TNBC-related metastasis machinery, we also compared the lncRNA profiles of TNBC tumor tissues to that of luminal breast tumor tissues.Then, the lncRNAs, MIF-AS1, PRNCR1, and Uc003xsl.1, were also highly expressed in TNBCs in comparison to those of luminal tumors and were selected for further exploration.

overall_design: Examination  the lncRNA profiles of TNBC tumor tissues to that of luminal breast tumor tissues.


title: Transcriptome analysis the early and advanced stage of ovarian cancer

city: Changchun

first: Lixin

last: Chen

address: 1266 Fujin Road

institute: Jilin University

summary: We aim to explore the common gene between proteomics and transcriptomics and pathway mechanism related to layer classification. Our results will provide several potential biomarkers in early diagnosis of ovarian cancer.Transcriptomics methods were performed to compare the differences between early ovarian cancer specimens (n = 3, stage Ⅰ / Ⅱ) and advanced ovarian cancer specimens (n = 6, stage Ⅲ / Ⅳ), and the similarities and differences of the data obtained were analyzed.

overall_design: F0482, F0492 and F0512 are the early ovarian cancer tissue. F0531, F0532, F0557, F0564, F0568 and F0575 are the advanced ovarian cancer tissue.


title: Changes in nuclear lamin-B stability marks the onset of aging in Drosophila

city: Singapore

first: Chin Tong

last: Ong

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: In this study, we showed that reduced nuclear lamin-B marks the onset of physiological decline in young adult Drosophila and its ectopic expression in dopaminergic neurons is sufficient to improve their locomotor activity during aging. Furthermore, the decline in lamin-B protein appeared to be unrelated to its mRNA level. Instead, we found drastic changes to its protein solubility during aging. Given the importance of nuclear lamin-B in genome organization and the advancement of single-cell epigenome profiling technology, our findings provide the community the basis to further study how altered level of lamin-B protein may elicit changes in gene expression that can contribute to the onset of physiological decline in animals.

overall_design: Comparison of differentially expressed genes in Day 30 adult lamin-B overexpressing and control sibling fly heads (2 replicates).

first: Chin-Tong

first: Wei-Qi

last: Lin


title: NanoString PanCancer Immune Profiling of 4′‐bromo‐resveratrol treated BrafV600E/PtenNULL melanoma mice

city: Madison

first: Nihal

last: Ahmad

state: Wisconsin

address: WIMR II, 1111 Highland Ave

department: Dermatology

institute: University of Wisconsin

summary: We performed differential gene expression analysis using high throughput multiplex analysis via NanoString nCounter PanCancer Immune Profiling panel, which analyzes 770 genes related to cancer-immune pathways (cancer progression, chemokines and cytokines and their receptors, and innate and adaptive immune response). nSolver software was used to analyze the data and a heat map was generated to show differential expression of 770 genes. Further, using a fold cut-off of ≥2 and p-value <0.05, we observed that 4'-BR significantly modulated expression of multiple cancer immune genes.

overall_design: Tumors were induced by topical application of 4-hydroxy-tamoxifen on shaved backs of 10-week-old mice, and the effects of 4′‐BR (30 mg/kg b.wt.; intraperitoneally; 3d/week for 5 weeks) were assessed on melanoma development and progression. RNA was extracted from tumors obtained from control and 30 mg/kg 4′‐BR treated mice (n = 6), followed by determination of expression of 770 genes (730 immune genes and 40 housekeeping genes) via the Mouse PanCancer Immune Profiling Panel using the nCounter platform in the NanoString Technologies .

first: Gagan

last: Chhabra

first: Chandra

middle: K

last: Singh


title: Ribo-seq (Ribosome profiling) analyses in human multiple myeloma cells

city: Nanjing

first: Rong

middle: Fang

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

summary: Detection of protein translation status at the gene level. Ribo-seq experiment of human multiple myeloma cells including NAT10 overexpression and controls were conducted.

overall_design: To identify the protein translation level in the  human multiple meloma cells

first: Rongfang


title: Transcriptome and N4-acetylcytidine RNA acetylation analyses in human multiple myeloma cells

summary: To identify the ac4C acetylation in the  human multiple meloma cells  .acRIP-seq and RNA-seq experiments of human multiple myeloma cells including NAT10 overexpression and controls were conducted.


title: KMT9 controls growth and stemness of colorectal cancer [ChIP-seq]

city: Freiburg

first: Christopher

last: Berlin

address: Hugstetter Straße 55

country: Germany

institute: University Hospital Freiburg

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The aim of the study is to identify KMT9a target genes in AOMDSS tumour organoids

overall_design: ChIP-seq

first: Roland

last: Schüle

first: Félicie

last: Cottard

first: Dominica

last: Willmann


title: Next Generation Sequencing Fascilitates Quantitative Analysis of Differential Gene Expression in Human Pericytes treated with PDGF-BB

city: Auckland

first: Leon

last: Smyth

address: 85 Park Road

country: New Zealand

institute: University of Auckland

summary: PDGF-BB:PDGFRβ signalling in brain pericytes is critical to the development, maintenance and function of a healthy blood-brain barrier (BBB). Furthermore, BBB impairment and pericyte loss in Alzheimer’s disease (AD) is well documented. We used tissue microarrays from control and AD brains to determine if PDGF-BB:PDGFRβ signalling components were altered in AD, and found that there was a reduction in vascular expression of PDGFB. We hypothesised that reduced PDGF-BB:PDGFRβ signalling in pericytes may have an impact on functions related to the BBB. We therefore tested the effects of PDGF-BB on primary human brain pericytes in vitro to define important signalling pathways and outcomes related to BBB function. Pericytes demonstrate a biphasic response to PDGF-BB, predominantly dependent on Akt and ERK. We determined that the actions of PDGF-BB are on-target at PDGFRβ, leading to internalisation and degradation of PDGFRβ. Using pharmacological inhibitors, we dissected distinct aspects of the PDGF-BB response that are controlled by ERK and Akt pathways. PDGF-BB promotes the proliferation of pericytes and protection from toxic stimuli through ERK signalling. In contrast, PDGF-BB:PDGFRβ signalling through Akt and NF-κB augments pericyte-derived inflammatory secretions. It may therefore be possible to supplement PDGF-BB or small molecule agonists to stabilise the cerebrovasculature in AD.

overall_design: mRNA profiles of post-mortem human pericytes treated with PDGF-BB at 1hr and 24hr

middle: C

first: Jane

last: Wu

first: Maurice

last: Curtis

first: Richard

middle: L

last: Faull

first: Mike

last: Dragunow


title: Key genes during ethylene-induced adventitious root development in cucumber (Cucumis sativus L.)

city: Lanzhou

first: Weibiao

last: Liao

address: 1 Yinmen Village, Anning District

institute: Gansu Agricultural University

summary: Our previous studies have shown that exogenous ethylene (ETH) may induce plant adventitious root development in cucumber. In this study, transcriptome technique was used to explore the key genes in ETH-induced rooting. The results revealed that ETH regulated 1415 diferentially expressed genes (DEGs) during rooting, among which 687 DEGs were up-regulated and 728 DEGs were down-regulated. According to Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, the critical pathways involved in ETH-induced adventitious root development were selected for further study, including carbon metabolism [starch and sucrose metabolism, glycolysis / gluconeogenesis, citrate cycle (TCA cycle), oxidative phosphorylation, fatty acid biosynthesis and fatty acid degradation], secondary metabolite biosynthesis (phenylalanine metabolism and flavonoid biosynthesis) and plant hormone signal transduction.  In carbon metabolism, ETH reduced t the expression of CsHK2, CsPK2 and CsCYP86A1, whereas enhanced the expression of CsBAM1 and CsBAM3. Moreover, ETH negatively regulated the transcript level of CsPAL and CsF3’M and positively mediated that of CsPAO in secondary metabolite biosynthesis pathway. Additionally, ETH could induce adventitious rooting by negatively regulating auxin and ETH signal transduction-related genes (CsLAX5, CsGH3.17, CsSUAR50 and CsERS) and positively regulating ABA and BR signaling transduction-related genes (CsPYL1, CsPYL5, CsPYL8, CsBAK1 and CsXTH3) . Furthermore, the results of real-time PCR about the mRNA levels of these genes were consistent with transcriptome results. Therefore, ETH may induce adventitious root development by regulating carbon metabolism-related genes, secondary metabolite biosynthesis-related genes and plant hormone signal transduction-related genes.

overall_design: Cucumber explants at 48 h after the control (distilled water) and  ethylene donor (0.5 μM ethrel) tratments were collected and stored at −80 °C until being used, in triplicate, and RNA was extracted and sequenced by paired-end sequencing, using Illumina.

first: Yuzheng

last: Deng

first: Chunlei

last: Wang


title: LncRNA Uc003xsl.1 Activates NF-κB/IL8 Axis to Promotes Triple-negative Breast Cancer Progression via A Decoy Role to NKRF

first: huang

last: liang

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: KMT9 controls growth and stemness of colorectal cancer [single-cell RNA-seq]

summary: The aim of the study is to identify cell-specific KMT9a target genes in AOMDSS tumour organoids

overall_design: 2 samples (control & KO of KMT9a) of AOM/DSS tumour organoids were used for scRNA-seq

first: Stephan

last: Tirier


title: Gene expression data of winter wheat root under drought stress for 7 days by two phosphorus treatments

city: Shihezi

first: Xiangchi

last: Zhang

address: Beisi Road, Shihezi, Xinjiang

institute: Shihezi University

summary:
A complex regulatory network is the mechanism of wheat roots responding to drought stress at low and adequate phosphorus levels.  The transcription levels of genes encoding silicon transporters, phosphate transporters, sucrose synthesis, etc., are mostly up-regulated in Xindong20. The genes encoding the electron transport chain and the respiratory chain are mostly down-regulated in Xindong23. These results suggest that wheat roots should maintain the structural integrity of the cells and reduce the energy metabolism during the coupled stress of drought and low phosphorus, which will help to improve the drought tolerance of wheat.
The objective of the present data was to increase the information about the effect of drought on the transcriptomes of wheat root cultured by two phosphorus levels.

overall_design: To study the transcriptional responses of two winter wheat (Xindong20 and Xindong23) roots under drought stress during two phosphorus (conventional phosphorus level (CP: 1.0 mmol /L) and low phosphorus level (LP: 0.05 mmol /L))  treatments. The total RNA of the root sampled from two phosphorus treatments at 7d under drought stress was extracted and carried out the following gene chip experiments. Additionally, three biological replicates were performed in this study to reduce the errors caused by biological differences and ensure the accuracy and reliability of gene chip data.

first: Weidan

last: Lu

first: Xiaoli

first: Bin

last: Ma

first: Kaiyong

last: Fu

first: Cheng

last: Li

first: Chunyan


title: Stem cells expand potency and alter tissue fitness by accumulating diverse epigenetic memories (ATAC-seq)

city: New York

first: Kevin Andrew

middle: Uy

last: Gonzales

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Immune and tissue stem cells retain an epigenetic memory of inflammation that intensifies sensitivity to future encounters. Here, we address whether and to what consequence stem cells possess and accumulate memories of diverse experiences. Monitoring a choreographed response to wounds, we find that as hair follicle stem cells leave their niche, migrate to repair damaged epidermis and take up long-term foreign residence there, they accumulate long-lasting epigenetic memories of each experience, culminating in post-repair epigenetic adaptations that sustain the epidermal transcriptional program and surface barrier. Each memory has its own physiological impact, collectively endowing these stem cells with heightened regenerative ability to heal wounds and broadening their tissue regenerating tasks compared to their naïve counterparts. These findings have profound implications for tissue fitness and aging.

overall_design: We use ATAC-seq technology to delineate open chromatin states across homeostatic, wound-induced and niche-adapted SC populations in the skin in vivo. By looking at differences in chromatin accessibility through time, we identify regions that open and close as cells undergo plasticity and enter a new niche, including those that correspond to memories of their prior experiences.

first: Kevin-Andrew

middle: U

first: Elaine

last: Fuchs


title: The influence of early life stress on social behavior and transcriptome in the prefrontal cortex.

city: Suita

first: Noriyoshi

last: Usui

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

summary: Early life stress (ELS), such as neglect and maltreatment, exhibits a strong impact on the mental and brain development of children. However, it is not fully understood how ELS affects the function in developing prefrontal cortex (PFC). In this study, we performed social isolation on weaned pre-adolescent mice and investigated how ELS could affect the function in behavior and transcriptome in PFC. We found that reductions of social interaction, social preference, and social novelty in ELS mice. Moreover, an increase of anxiety-like behavior was observed in ELS mice, but there were no changes in weight and repetitive behavior. To identify the gene involved in social behavior, we conducted transcriptome analysis and identified 15 differentially expressed genes (DEGs) in the PFC of ELS mice. These genes were involved in transcriptional regulation, stress, and synaptic signaling. We also found that a decreased number of neurons and an increased number of microglia in the PFC of ELS mice. These results suggest that ELS affects PFC cytoarchitecture by stress signal transduction and eventually alters mouse behavior. Our study demonstrates that ELS influences behavior, transcriptome and cytoarchitecture in the brain of adolescent mice.

overall_design: ELS and control mice at 9 weeks age were used. Each group contains 3 mice. RNA-seq were conducted using RNAs extracted from prefrontal cortex of these mice.

first: Ryoko

last: Aramaki

first: Yuta

last: Ono

first: Stefano

last: Berto

first: Genevieve

last: Konopka

first: Hideo

last: Matsuzaki

first: Shoichi

last: Shimada


title: miCLIP in METTL14 R298P mutation knock-in cell clones

first: Atsushi

last: Kumanogoh

state: Osaka

type: Methylation profiling by high throughput sequencing

summary:
N6-methyladenosine (m6A) is the major type of RNA modi'cation that regulates RNA stability and gene expression, characterized by a conserved motif including 5'-(m6A)C-3'. However, the functional significance of the specific motif for m6A modification is unclear.
Here, we focused on a single amino acid substitution in the m6A 'writer' complex, METTL14 R298P, and created mutation knock-in cells.
m6A individual-nucleotide-resolution cross-linking and immunoprecipitation and methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) revealed that METTL14R298P/R298P but not METTL14WT/R298P cells had an aberrant sequence motif, 5'-(m6A)[C/T]-3'. This study reveals a mechanism underlying sequence-specific m6A modification.

overall_design:
miCLIP analysis was performed in METTL14 R298P mutation knock-in cell clones.
METTL14 R298P mutation knock-in cell clones were established from HEC108 cell line. miCLIP analysis was performed on poly(A)-purified mRNA in HEC108_ki042 clone (METTL14+/+), HEC108_ki004 clone (METTL14+/R298P), and HEC108_ki047 clone (METTL14 R298P/R298P).

first: Kotaro

last: Miyake

first: Yuki

last: Kato

first: Yukio

last: Kawahara


title: RNA-Seq of MDA-MB-231 cells treated with 1-SO (2,8-diacetoxymethyldibenzothiophene-S-oxide) and 1-S (2,8-diacetoxymethyldibenzothiophene) under variable UV conditions

city: Saint Louis

first: Ryan

last: McCulla

state: Missouri

address: 3501 Laclede Ave

department: Chemistry

institute: Saint Louis University

summary:
RNA-Seq analysis to assess gene expression levels in MDA-MB-231 cells on treatment with 1-SO (2,8-diacetoxymethyldibenzothiophene-S-oxide) and 1-S (2,8-diacetoxymethyldibenzothiophene) under variable UV conditions
We report the gene expression levels in MDA-MB-231 cells on treatment with 1-SO (2,8-diacetoxymethyldibenzothiophene-S-oxide) and 1-S (2,8-diacetoxymethyldibenzothiophene) under 30 minute UV-A irradiation (UV) and no UV-irradiation/dark (No-UV)

overall_design: MDA-MB-231 cells (600,000 cells/1.8mL/well) were plated on a six-well plates. The plates were incubated with compounds (10uM-final concentration) for 24 hours (VC - 1% DMSO). For UV experiment, one plate was placed in a Luzchem photoreactor equipped with 8 LZC-UVA bulbs  (fwhm, 325-375 nm) for 30 minutes and for the No_UV experiment, the plate was covered with an aluminum foil for 30 minutes. RNA was then extracted  using a total purification RNA kit (Sigma Aldrich - Catalog #RNB100) based on the associated protocol. Novogene Corporation performed sequencing and associated bioinformatics analysis.

first: Ankita

last: Isor

first: Scott

middle: F

last: Grady

first: Christopher

last: Arnatt

middle: D


title: The expression profiles of microRNAs in prostate epithelial cells

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

institute: Capital Medical University

summary: MicroRNAs (miRNAs) are non-protein-coding small RNAs in the size range 19–25 nucleotides (nt) that are cleaved from 70-100 nt hairpin pre-miRNA precursors.MiRNAs bind to complementary sequences in the 3′-untranslated regions of their target mRNAs and induce mRNA degradation or translational repression. Recent intensive studies have revealed that miRNAs play important roles in a large number of biological processes, including cellular differentiation, proliferation and death. These wide-ranging biological roles suggest that miRNAs may be involved in cancer development. MiRNAs regulate a variety of biological processes, including developmental timing, signal transduction, cell growth, and cell death.

overall_design: RNA labeling and hybridization were completed by KangChen Bio-tech Inc. (Shanghai, China) according to the manufacturer's instructions. Briefly,Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions. After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0) which contains probes for 3100 mature miRNA.Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner.Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

first: kong

last: lu


title: Distinct miR Expression Signatures of Primary and Secondary CNS Lymphomas

city: Budapest

first: Endre

last: Sebestyén

address: Üllői út 26.

department: 1st Department of Pathology and Experimental Cancer Research

country: Hungary

institute: Semmelweis University

summary: FFPE brain biopsy specimens of 64 patients with primary central nervous system lymphoma and 9 patients with secondary central nervous system lymphoma were analyzed in the study. We used the NanoSting nCounter human v3 miRNA assay for characterizing miRNA expression and carried out a detailed differential expression and clustering analysis of samples and miRNAs to look for expression changes associated to primary or secondary origin, cell of origin, mutation status or survival.

overall_design: FFPE brain biopsy specimens of 64 patients with primary central nervous system lymphoma (PCNSL) and 9 patients with secondary central nervous system lymphoma (SCNSL) were analyzed in this study. Tissue samples were obtained from three different centers.

first: Ákos

last: Nagy

first: Dóra

last: Marosvári

first: Hajnalka

last: Rajnai

first: Béla

last: Kajtár

first: Beáta

last: Deák

first: András

last: Matolcsy

first: Sebastian

last: Brandner

first: James

last: Storhoff

first: Chen

last: Ning

first: Attila

middle: G

last: Bagó

first: Csaba

last: Bödör

first: Lilla

last: Reiniger


title: KMT9 controls growth and stemness of colorectal cancer [RNA-Seq]

last: Berlin

summary: The aim of the study is to identify KMT9α target genes in AOM/DSS tumour organoids, APK and APKK organoids, patient derived CRC organoids, AOM/DSS mouse tumours and normal mouse colon

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: AOM/DSS tumour organoids, APK and APKK organoids, patient derived CRC organoids +/- KMT9α, AOM/DSS tumours and benign epithelial colon cells from mice, all files are independent biological replicates

first: Roland

last: Schüle

first: Félicie

last: Cottard

first: Dominica

last: Willmann


title: Transcription profiling of MamBo cell lines

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: We studied cell lines derived from two transgenic mammary tumors driven by human HER2 that showed different dynamics of HER2 status. MamBo89 (HER2 stable) cell line displayed high and stable HER2 expression, which was maintained upon in vivo passages, whereas MamBo43 (HER2 labile) cell line gave rise to HER2-negative tumors, from which MamBo38 (HER2 loss) cell line was derived. MamBo cell lines were established from mammary tumors of FVBhuHER2 virgin female mice.

overall_design: Transcription analysis was performed on the three cell lines with and without treatment with trastuzumab.

first: Veronica

last: Giusti

first: Francesca

last: Ruzzi

first: Lorena

last: Landuzzi

first: Marianna

last: Ianzano

first: Roberta

last: Laranga

first: Elena

last: Nironi

first: Laura

last: Scalambra

first: Giordano

last: Nicoletti

first: Carla

last: De Giovanni

first: Martina

last: Olivero

first: Maddalena

last: Arigoni

first: Patrizia

last: Nanni

first: Arianna

last: Palladini

first: Pier-Luigi

last: Lollini


title: KMT9 controls growth and stemness of colorectal cancer

first: Christopher

last: Berlin


title: LncRNA Uc003xsl.1 Activates of NF-κB/IL8 Axis to Promotes Triple-negative Breast Cancer Progression via A Decoy Role to NKRF [ChIP-Seq]

first: huang

last: liang

summary: We explore the NF-κB responsive transcription that was regulated by Uc003xsl.1/NKRF complex. The chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) was performed for NKRF in MDA-MB-231-P3 cells treated with si-Uc003xsl.1 or control siRNA. The ChIP-seq data displayed 3604 peak calls in MDA-MB-231-P3 cells against control siRNA and were primarily identified as NF-κB targeting genes.

first: Ying

last: Xu

first: Qingjian

last: Li

first: Chaohui

last: Duan

first: Herui

last: Yao


title: The ratio of periportal mesenchyme to ductal epithelium acts as a proliferative rheostat in liver regeneration

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Liver epithelial cells –hepatocytes and bile duct cells– intermingle with a microenvironment of endothelial cells, macrophages and fibroblasts to form the functional unit of the tissue.  In homeostasis, the liver epithelium self-renews slowly, yet it is capable of remarkable regeneration following damage. We have shown that liver ductal cells can be expanded in vitro under defined medium to form 3D epithelial 'liver organoids' that recapitulate many aspects of the regeneration process in vitro, yet lack stromal cell components. Here, we describe that a subpopulation of portal mesenchymal cells expressing Sca1 and Pdgfra, exerts a dual effect on the proliferative capacity of ductal cells. On one hand, it supports liver organoid formation and expansion in the absence of exogenous growth factors and independently of cell-to-cell contact. However, when Ductal cells and SCA1+ mesenchymal cells establish physical interaction following a microfluidics encapsulation that enables the cells to self-organize into chimeric organoid structures, cell proliferation is abolished in a mesenchymal-dose dependent manner. We found that it is the ratio between mesenchyme and epithelial cells and not their absolute values that determines the net outcome of ductal proliferation both in vitro, and in vivo, during the different phases of liver regeneration. The mechanism by which Sca1+ mesenchymal cells regulate ductal cell proliferation dynamics is mediated, at least in part, by Notch cell-cell contact inhibition. Our findings underscore how the relative ratio and distribution of cell-cell contacts between the epithelium and its mesenchymal microenvironment are key regulatory processes during the dynamic regulation of tissue regeneration.

overall_design: RNA profile of ductal and mesenchymal cells sorted from healthy adult mouse livers and analysed at t=0 or after 15 days of in vitro culturing

first: Meritxell

last: Huch

first: Lucía

last: Cordero-Espinoza

first: Anna

last: Dowbaj

first: Clare

last: Pacini


title: Anoctamin 5 regulates the cell cycle and affects prognosis in gastric cancer

city: Kyoto city

first: Tomoyuki

last: Fukami

state: (None)

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary: Anoctamin 5 as a key mediator in tumor progression, it may being a promising prognostic biomarker for a novel therapeutic target of GC.

overall_design: Total RNA of NUGC4 cells were extracted using an RNeasy kit (Qiagen, Valencia, CA, USA). Real-time quantitative PCR (The Step One plus Real-Time PCR System; Applied Biosystems, Foster City, CA) and TaqMan Gene Expression Assays (Applied Biosystems) were employed. We compared the differences in gene expression between negative control and knockdown of anoctamin 5 in NUGC4 cells using Microarray assay.

first: Atsushi

last: Shiozaki

first: Toshiyuki

last: Kosuga

first: Michihiro

last: Kudou

first: Hiroki

last: Shimizu

first: Takuma

last: Ohashi

first: Tomohiro

last: Arita

first: Hirotaka

last: Konishi

first: Shuhei

last: Komatsu

first: Takeshi

last: Kubota

first: Hitoshi

last: Fujiwara

first: Kazuma

last: Okamoto

first: Mitsuo

last: Kishimoto

first: Yukiko

last: Morinaga

first: Eiichi

first: Eigo

last: Otsuji


title: LncRNA Uc003xsl.1 Activates of NF-κB/IL8 Axis to Promotes Triple-negative Breast Cancer Progression via A Decoy Role to NKRF [RNA-Seq]

city: chengdu

first: huang

last: liang

address: No.24, South First Section, First Ring Road, Wuhou District, Chengdu City

institute: sicuan university

summary: The RNA-seq analysis was also performed on MDA-MB-231-P3 cells transfected with control or Uc003xsl.1 siRNA. A gene signature with highly significant expression changes post-Uc003xsl.1 siRNA treatment was observed

overall_design: Examination the differentiated expression genes in MDA-MB-231-P3cells after downregulation of Uc003xsl.1

first: Ying

last: Xu

first: Qingjian

last: Li

first: Chaohui

last: Duan

first: Herui

last: Yao


title: Smad4 modulates expression of chemokine receptor Ccr6 in mouse colon stroma

city: Nashville

first: David

last: Hanna

state: Tennessee

address: 1211 Medical Center Drive

institute: Vanderbilt University Medical Center

summary: Purpose: To understand how loss of epithelial Smad4 alters gene expression in mouse colon stroma  Methods: To understand the extent of Smad-mediated gene regulation in the colon, we isolated colon epithelium from three Smad4ΔLrig1 and from three SMAD4+ control mice (either mice lacking a CreERT allele and treated with tamoxifen, or mice bearing a CreERT allele but treated with vehicle only) and analyzed the colonic stroma by RNAseq.  Results: A comparison of gene expression within the sub-epithelial stroma of Smad4Lrig1 mice relative to SMAD4+ control mice demonstrated a marked increase in inflammatory gene signaling. Of the 95 genes that were upregulated by at least 2.5-fold (≥1.32 Log2 Fold Change) and a false discovery rate <0.05, 51 genes are known to be expressed on immune cells or have immune-related functions, including Ccr6.  Conclusions: SMAD4 modulates inflammatory signaling in colonic stroma to repress colitis-associated tumor formation

overall_design: Three Smad4Lrig1 and three SMAD4+ control mice were dissected 1 month after administration of tamoxifen. Colon crypts were chelated using Ethylenediaminetetraacetic acid (EDTA). Following crypt chelation, the sub-epithelial stroma was removed from the underlying muscle layer by scraping. RNA was then made from the sub-epithelial stroma using RNeasy kit (Qiagen, Germantown, MD) and RNA-seq performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core facility. 32–37 million 51–base pair, single-end reads were generated per sample. Reads were mapped to the mouse genome mm10 using TopHat-2.1.0, uniquely mapping 86%–95% single-end reads to the genome, depending on the study. The number of reads that fell into annotated genes were counted using samtools-1.3.1 and HTSeq-0.5.4p5. Count-based differential expression analysis was performed using edgeR_3.4.2.

middle: N

first: Paula

middle: M

last: Smith

first: Sergey

last: Novitskiy

last: Washington

first: Chanhuan

last: Shi

first: Jinhuan

last: Zi

first: Connie

last: Weaver

first: Jalal

last: Hamaamen

first: Keeli

middle: B

last: Lewis

first: Jing

last: Yang

first: Qi

last: Liu

first: Robert

last: Beauchamp

first: Anna

last: Means


title: Expression data from HCC1954 cells treated with DMSO, Melatonin (mela), Lapatinib (lapa) and their combination(m_l)

city: Dalian

first: Hailing

last: Cheng

address: 467 Zhongshan Road

institute: The Second Hospital of Dalian Medical University

summary: Drug treatment-induced transcriptional changes in HCC1954 cells.

overall_design: HCC1954 breast cancer cells were treated with DMSO, Melatonin (mela, 2mM), Lapatinib (lapa, 1uM) and their combination (m_l) for 24 hours, followed by RNA extraction and RNA sequencing analysis. Each has three biological repeats.

first: Xiaolin

last: Sang

first: Pixu


title: Identification and application of a panel of constitutive promoters for gene overexpression in Staphylococcus aureus

city: Chengdu

first: Qiang

address: Guoxue street 37

institute: West China Hospital, Sichuan University

summary: Staphylococcus aureus is a leading pathogen that is currently the most common cause of infection in hospitalized patients. An in-depth genetic analysis of S. aureus virulence genes contributing to pathogenesis is needed to develop novel antimicrobial therapies. However, tools for genetic manipulation in S. aureus are limited, particularly those for gene expression. Here, 38 highly expressed genes were identified in S. aureus USA300_FPR3757 via RNA-seq. Promoter regions from 30 of these genes were successfully cloned, of which 20 promoters exhibited a wide range of activity. By utilizing these active promoters, 20 S. aureus-E. coli shuttle vectors were constructed and evaluated by expressing an egfp reporter gene. Expression of egfp gene under the control of different promoters was confirmed and quantified by Western-blot and qPCR, which suggested that the activity of these promoters varied from 18% to 650% of the activity of PsarA, a widely used promoter for gene expression currently. In addition, our constructed vectors were verified to be of high compatibility on gene expression in different S. aureus strains. Furthermore, these vectors were evaluated and used in overexpressing two endogenous proteins in S. aureus, namely, catalase and the transcriptional repressor of purine biosynthesis (purR). Meanwhile, the physiological functions and phenotypes of overexpressed purR and catalase in S. aureus were validated. Altogether, this evidence indicates that our constructed vectors provide a wide range of promoter activity on gene expression in S. aureus. This developed system will provide a powerful tool for the direct analysis of target gene function in staphylococcal cells.

first: Daiyu

last: Li

first: Quanming

last: Zou

first: Xiaokai

last: Zhang


title: Exploring gene expression signatures of itraconazole for infantile hemangioma endothelial cell in vitro

city: chongqing

first: shuang

last: chen

address: No. 1 Youyi Road, Yuzhong District

institute: the First Affiliated Hospital of Chongqing Medical University

summary: In order to understand the mechanisms underlying the effects of itraconazole in infantile hemangioma endothelial cells, we further explored the potential targeting genes of itraconazole in infantile hemangioma endothelial cells in vitro by using a genome-wide gene expression array. In total 172 mRNAs were up-regulated (fold change > 2) and 819 mRNAs were down-regulated (fold change > 2) upon itraconazole treatment in infantile hemangioma endothelial cells. The top signaling pathway closely related to differentially expressed genes upon itraconazole treatment is the cytokine and cytokine receptor pathway. Within this pathway, the mRNA expression of PDGF-D, an important growth factor belonging to the PDGF family, was the most significantly reduced (30 folds) among 991 differentially expressed genes after itraconazole treatment. qRT-PCR and western blotting  confirmed the inhibitory effects on PDGF-D levels.

overall_design: Infantile hemangioma endothelial cells from 2 infants were treated with 10μM itraconazole or 0.1% DMSO for 48 hours.  Total mRNAs were extracted used for mRNA array analysis with Agilent's Human (V2) Gene Expression Microarray  (8×60K chip), according to the manufacturer’s instructions.

first: Shuang

last: Chen

first: Yuping

last: Ran


title: Differential gene expression analysis on cells expressing Wild type GFP-MAB21L1 and its mutant form GFP-Arg51Leu and GFP-Arg51Gln

status: Public on Nov 27 2021

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

summary: RNA Sequencing analysis was performed on RNA isolated from cells tagged with GFP-MAB21L1 and its mutant form GFP-Arg51Leu and GFP-Arg51Gln with and without treatment of tetracycline for 12 hrs. Transcript-level quantitation was performed using Salmon (v0.8.2) against the GRCh38 Ensembl reference transcriptome (release-89).Transcript-level counts were summarized to gene level using the bioconductor package tximport (v1.4.0). Differential expression analysis was performed with the bioconductor package DESeq2 (v1.30.0) using the Wald significance tests.

overall_design: 12 samples , with 6 groups and 2 replicates per group.

middle: R

first: Hemant

last: Bengani


title: Polycomb repressive complex 1 (PRC1) role in lingual epithelium development [ChIP-Seq]

status: Public on Nov 28 2021

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

summary: Polycomb repressive complexes (PRC) 1 is essential for the maintenance of lingual papillae pattern.

overall_design: Lingual epithelium was purified from newborn control mice by FACS sorting.  Immunoprecipitated chromatin was analyzed by ChIP-seq.

first: Carmit

last: Bar

first: Deyou

last: Zheng

first: Elena

last: Ezhkova


title: Genome-wide maps of mRNAs and ncRNAs in aging and young dental pulp stem cells

city: Tianjin

first: XIAOCAO

last: MA

address: Medical Collage of Nankai University

institute: Nankai University

summary:
Purpose: The goals of this study are to compare differentially expressed genes in young dental pulp stem cells to the aging dental pulp stem cells and to predict key regular factors.
Methods: mRNA and ncRNA profiles of young and aging dental pulp stem cells were generated by deep sequencing, using BGISEQ-500 platform (BGI-Shenzhen, China). The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Agilent Technologies 2100 system and real-time quantitative PCR (QPCR) (TaqMan Probe).
Results:After filtering out adaptor-related and low-quality sequences, 669 million clean reads in mRNA Library were generated. Clean reads was mapped to genome sequence with the mapping ratio from 88.54% to 97.61%. A total of 230487 mRNAs was obtained including 123724 known mRNAs and 106763 novel mRNAs respectively; In addition, we detected 177880 lncRNAs，139743 and 38137 were known and novel. For correlation analysis, the coefficient we obtained were all greater than 0.90, indicating a high biological correlation
Conclusions: Our study represents the first detailed analysis of differentially expressed genes in aging and young dental pulp stem cells, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that hsa-miR-6724-5p may be a key node in the aging process of DPSCs, and its target genes was involved in the dopaminergic synapse

overall_design: mRNA and ncRNA profiles of aging and young dental pulp stem cells

first: RONG

last: ZHANG

first: E

last: LINGLING

first: HONGCHEN

last: LIU


title: Modeling OTUD7A loss-of-function mutation in schizophrenia-associated 15q13.3 microdeletion in human neurons

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: The edited lines introduced a premature termination at rs757148409/p.Arg89Ter. The mutant iNs showed a ~50% decrease in OTUD7A protein expression without undergoing nonsense-mediated mRNA decay. The mutant iNs also exhibited marked reduction of dendritic complexity, synaptic puncta density of AMPA receptor subunit GluA1 and postsynaptic scaffold PSD-95, as well as neural firing rate and network activity. Congruent with the neural phenotypic alterations in mutant iNs, our transcriptomic analysis showed that the set of OTUD7A LoF downregulated genes was significantly enriched for synapse development and function, and was associated with SZ and other neuropsychiatric disorders. These results suggest that the OTUD7A LoF mutation rs757148409 impairs neurodevelopment and synaptic function in human neurons, providing mechanistic insight into the possible role of OTUD7A in driving neuropsychiatric phenotypes associated with the 15q13.3 microdeletion.

overall_design: Identifying causative gene(s) within large genomic regions of copy number variants (CNVs) associated with neuropsychiatric disorders is challenging. Otu deubiquitinase 7a (Otud7a) knockout mice recapitulate some phenotypes associated with the 15q13.3 microdeletion syndrome, leading to the hypothesis that OTUD7A is the driver of this CNV’s neuropsychiatric phenotypes. Here, by targeted sequencing of 1,779 SZ cases and 1,418 controls we identified three putative OTUD7A loss-of-function (LoF) mutations in cases, but none in controls. We then modeled one of these OTUD7A LoFs, rs757148409, in human induced pluripotent stem cell (hiPSC)-derived induced excitatory neurons (iNs) by CRISPR/Cas9 engineering.

first: Alena

last: Kozlova

first: Siwei


title: Polycomb repressive complex 1 (PRC1) role in lingual epithelium development [RNA-seq]

overall_design: Lingual epithelium was purified from E16 control and Ring1a/b 2KO embryos by FACS sorting. RNA from the sorted cells was analyzed by RNA-seq.


title: Polycomb repressive complex 1 (PRC1) role in lingual epithelium development

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: A Tumour-Resident Lgr5+ Stem Cell - Like Pool Drives the Establishment and Progression of Advanced Gastric Cancers

status: Public on Nov 26 2021

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

institute: Singapore Immunology Network (SIgN)

summary: Gastric cancer is amongst the most prevalent and deadliest cancers globally. To derive mechanistic insight into the pathways governing this disease, we generated a stomach-specific Claudin18-IRES-CreERT2 mouse line to model advanced human gastric cancer and investigated the role of tumour resident Lgr5+ stem-like cells in gastric cancer. Mouse lines incorporating Cldn18-driven conditional dysregulation of the Wnt, RTK and Trp53 pathways modelled metastatic Chromosomal Instable-type gastric cancer. In parallel, we supplemented these cancer models with orthotopic transplantation of cancer organoids to derive detailed mechanistic insight into the roles of Lgr5+ cancer stem cell in gastric cancer. Here we show, we recapitulated advanced human gastric cancer in terms of disease phenotype, aberrant gene expression profile, molecular markers, and sites of distant metastases. Importantly, we established that tumour-resident Lgr5+ stem-like cells are critical to the initiation and maintenance of tumour burden, and are obligatory for the establishment of metastases. These models will be invaluable for deriving clinically-relevant mechanistic insights into cancer progression and as pre-clinical models for evaluating novel therapeutics.

overall_design: Adult Cldn18-Apc(WT/Fl),Trp53(Fl/Fl),Kras(G12D) mice were induced with 100mg/kg tamoxifen. Tissue was harvested and tumours categorised as neoplastic or advanced/invasive. Tissue was lysed in Trizol and RNA extracted using Qiagen RNAEasy Kit. The libraries were constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® and sequenced on an Illumina NovaSeq 6000 platform at Novogene, Singapore.

first: Aliya

last: Fatehullah

first: Yumi

last: Terakado

first: Sowmya

last: Sagiraju

first: Bernett

last: Lee

first: Nick

last: Barker


title: Differences of miRMA expression signitures for blood samples of children with high blood lead level and low blood lead level

city: Xi'an

first: Changhao

last: Yang

address: 169 Changlexi Road

institute: Fourth military medical university

summary: To further explore the effect of blood lead on miRNA expression in blood, children (aged 2-5 years) from kindergartens of Shaanxi province were divided into two groups and blood samples were collected. miRNA array was used to testify miRNA expression landscape between low blood lead level (BLL) group (0~ 50.00 g/L) and high BLL group (>50.00 g/L).Our data showed that 27 miRNAs were highly differentially expressed. Expression of miR-34b from this signiture was quantified by qRT-PCR,linear regression analysis showed that the correlation coefficient between blood lead level and miR-34b is 0.247, p <0.001, indicating that miR-34b was correlated with BLL.

overall_design: For miRNA array, 40 children were randomly selected from high BLL group (n= 20) and low BLL group (n= 20). General characteristics, including age, body mass index (BMI) and gender between these groups showed no significant difference. 250 μL of blood samples from each subject were blended to form a 4 ml plasma pool of each group. Then, miRNA array analysis was carried out to compare differences in miRNA expression profiles between these two groups.

first: Peng

last: Su


title: Influence of IWS1 TND-interacting motifs (TIMs) on gene expression patterns [RNA-seq]

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: To reveal the influence of TND-interacting motifs (TIMs), which bind TFIIS N-terminal domains (TNDs), we prepared KELLY cells expressing either wild-type IWS1-FLAG or IWS1-FLAG containing disruptive mutations in the unstructured TIM3 region. Following lentiviral transduction of either WT or M3 IWS1-FLAG, we prepared mRNA from these samples and performed expression profiling using RNA-seq. Analysis of differential gene expression provided markers that are differentially regulated by TIM3 of IWS1.

overall_design: RNA-seq of KELLY cells expressing wild-type (WT) or mutant (M3) IWS1-FLAG via lentiviral transduction.

first: Katerina

last: Cermakova

first: H


title: MLK4 kinase regulates the DNA damage response and promotes triple-negative breast cancer chemoresistance

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Triple-negative breast cancer (TNBC) is a subtype of breast cancer characterized by the absence of estrogen and progesterone receptors, and the lack of HER2 amplification or overexpression. Chemoresistance is currently one of the major challenges in the treatment TNBC. Therefore, there is a need towards identification of the novel molecular targets that could be exploited to overcome TNBC chemoresistance. In this study, we found that knock-down of Mixed-Lineage Kinase 4 (MLK4), a member of MAP3K family of serine/threonine kinases, sensitizes TNBC cell to chemotherapy and impairs activation of DNA repair pathways upon genotoxic treatment. DNA damage response signaling network coordinates transcriptional response at multiple levels to preserve cellular homeostasis and promote survival in response to genotoxic stress.  Since MLK4-deficient cells were compromised for DNA damage response signaling activation following doxorubicin treatment, we hypothesized that the loss of MLK4 could significantly affect global transcriptomic changes induced by chemotherapy in TNBC cells. To test this hypothesis we performed gene expression profiling by mRNA-seq in HCC1806 TNBC cells transfected with control or MLK4-targeting siRNAs and treated with either 1 μM of doxorubicin for 24 h or vehicle only (DMSO control). Our RNA-seq analysis revealed that MLK4 is required for DNA damage-induced expression of several NF-кB-associated cytokines, including IL-6, which facilitates TNBC cells survival in an autocrine manner.

overall_design: mRNA-seq data from HCC1806 TNBC cell line transfected with MLK4-targeting (siMLK4) or control (siNT) siRNA, and treated with doxorubicin or vehicle only (DMSO) for 24h

first: Dawid

last: Mehlich

first: Anna

last: Marusiak

first: Dominika

last: Nowis


title: Hyperbilirubinemia and phototherapy differentially alter hippocampal transcriptomic patterns in a Gunn rat model of neonatal hyperbilirubinemia.

city: Minneapolis

first: Katherine

last: Satrom

state: MN

address: 516 Delaware St SE

institute: University of Minnesota

summary: Neonatal hyperbilirubinemia (jaundice) is common in infants, with extremely preterm infants (EPT, <28 weeks gestational age) being at high risk for bilirubin-induced neurotoxicity, resulting in neurodevelopmental impairment. Hyperbilirubinemia is treated using phototherapy to lower unconjugated bilirubin levels. However, the benefits and risks of phototherapy in EPTs have not been well studied, and bilirubin at low levels may be protective as an antioxidant. Phototherapy is associated with markers of oxidative stress in the plasma, but the effects of phototherapy on the hippocampus (HPC) are not known. Bilirubin and insults associated with EPTs impair hippocampal development, a brain structure critical for cognitive function, but their underlying mechanisms remain unknown. The effects of hyperbilirubinemia and phototherapy on the HPC were studied using a Gunn rat model. Jaundiced (jj) and non-jaundiced (Nj) pups were subjected to phototherapy from postnatal day 4 (P4) through P6. The HPC was harvested and processed for RNA sequencing. Serum bilirubin levels were elevated in jj compared to Nj control rats. Phototherapy significantly lowered serum bilirubin levels in jj rats. Compared to Nj rats, 1294 genes were differentially expressed in the jj hippocampal transcriptome and mapped onto the nervous system development, inflammation, and ferroptosis signaling pathways. Phototherapy induces 3297 differentially-expressed genes (DEGs) in rat hippocampal transcriptome compared to untreated rats. These DEGs were annotated to pathways regulating synaptogenesis, long-term potentiation, and neurogenesis. Both hyperbilirubinemia and phototherapy altered expression of 407 genes, which mapped onto hippocampal plasticity functions, including neuritogenesis and long-term potentiation. Our study demonstrates a model for investigating molecular effects of hyperbilirubemia and phototherapy in an EPT-equivalent Gunn rat pup. Our data revealed the effects of hyperbilirubinemia and phototherapy on signaling pathways critical for hippocampal development and plasticity.

overall_design: Gunn rat pups (non-jaundiced (Nj) controls and jaundiced (jj) pups (n=5/group ) were exposed to intermittent LED phototherapy from postnatal day 4 (P4) through P6.  Phototherapy was provided for a total of 12 hours (3 hours on/3 hours off during daytime hours). Untreated Nj and jj (n=6) were used as controls. Rats were killed on P6 using sodium pentobarbital (100 mg/kg, i.p.). A blood sample (250 µL) was collected via cardiac puncture. Hippocampal lobes were dissected on an ice-cold metal block, flash-frozen using liquid nitrogen, and stored at -80°C until analysis. Total RNA was isolated from one hippocampal lobe using RNAqueous Isolation kit (Ambion). Five rats were used per experimental group (Nj+No PT, jj+No PT, Nj+PT, jj+PT). RNA was further processed for sequencing.

first: Haeyeon

first: Eric

last: Lock

first: Troy

last: Lund

first: Phu

middle: V

last: Tran

first: Raghavendra

last: Rao


title: Silencing of UHRF1 in PC3 cells induces changes in the miRNome

city: Trento

first: Michela

middle: A.

last: Denti

address: Via Sommarive 9

department: Department of Cellular, Computational and Integrative Biology

institute: University of Trento

summary: To understand the role of UHRF1 in prostate cancer, we have employed miRNAs microarray expression profiling as a discovery platform to identify miRNAs whose expression is regulated by UHRF1 and have a potential to regulate downstream effectors involved in prostate cancer.

overall_design: PC3 cells were silenced with siRNAs against UHRF1 or control siRNAs, in triplicate, as previously described (Babbio F, Pistore C, Curti L, Castiglioni I, Kunderfranco P, Brino L, Oudet P, Seiler R, Thalman GN, Roggero E, Sarti M, Pinton S, et al. The SRA protein UHRF1 promotes epigenetic crosstalks and is involved in prostate cancer progression. Oncogene 2012;31: 4878-87).  RNA was collected 72 hours after transfection and knock-down of UHRF1 mRNA was validated by RT-PCR on each independent replicate sample.

first: Ian

last: Bonapace


title: Influence of IWS1 TND-interacting motifs (TIMs) on transcription elongation [PRO-seq]

summary: To reveal the influence of TND-interacting motifs (TIMs), which bind TFIIS N-terminal domains (TNDs), we prepared KELLY cells expressing either wild-type IWS1-FLAG or IWS1-FLAG containing disruptive mutations in the unstructured TIM3 region. Following lentiviral transduction of either WT or M3 IWS1-FLAG, we prepared PRO-seq libraries from these samples and examined elongation profiles. Analysis of elongation profiles revealed that TIM3 disruption induces pervasive defects of transcription elongation.

overall_design: PRO-seq of KELLY cells expressing wild-type (WT) or mutant (M3) IWS1-FLAG via lentiviral transduction.

first: Seth

last: Goldman

first: Karen

last: Adelman


title: Characterization of the IL23-IL17 immune axis in IBD patients

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: The aim of this study is to investigate the molecular mechanisms of IL23-IL17 immune axis in IBD, with particular attention to its role in maintaining mucosal barrier integrity under both physiological and pathological conditions

overall_design: n=84 biopsies from patients with Crohn's disease, n=40 biopsies from patient with Ulcerative colitis, and n=46 control biopsies

first: Silvia

last: D'alessio

first: Federica

last: Ungaro

first: Luigi

last: Lamparelli

first: Silvio

last: Danese


title: AMSC CD36+ subpopulations

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Adipose-derived MSCs (AMSC) are currently utilized in clinical trials for various diseases including osteoarthritis, amyotrophic lateral sclerosis, and multiple system atrophy. Whilst AMSCs may be defined by the surface expression of classical markers including CD44, CD90, CD105, and absence of CD45, these cells may exhbit donor-to-donor differences in differentiation potential. In this study we evaluated the expression of CD36 amongst AMSCs and utilized magnetic cell sorting to enrich for CD36+ cells. Whole transcriptome RNA-sequencing was performed on unsorted, CD36+ enriched, and CD36+ depleted cells to determine gene expression difference between these populations of cells. CD36 sorted or unsorted cells were then plated and maintained in growth medium. Cells were expanded for 2 passages and passage 8 cells were plated for RNA-sequencing analysis. Trizol reagent was used to harvest cells when they were proliferating cells (~80%) or 100% confluent cells.

overall_design: AMSC donors 540 and 536 were expanded using clinical grade standard operating protocols and harvested for RNA-sequencing analysis upon confluence. AMSC donor 211 at passage 5 was harvested for magnetic cell sorting using CD36-APC antibody and anti-APC magnetic microbeads. Magnetic sorting was performed on these cells and the postive (enriched) and negative (depleted) fractions were collected. Additionally, a portion of the CD36-APC-microbead labelled cells but not sorted cells were kept as an unsorted population. CD36+ sorted fractions and unsorted cells then plated and expanded under growth conditions. After 2 passages, cells at passage 8 were plated for RNA-sequencing analysis, and samples were harvsted when they were either proliferating (~80% confluent) or 100% confluent.

first: Andre

middle: J

last: van Wijnen

first: Emily

middle: T

last: Camilleri

first: Amel

last: Dudakovic


title: Alveolar epithelial type 2 cell RNA sequencing from SP-C BRICHOS mutation mouse model

city: Philadelphia

first: Apoorva

last: Babu

state: PA

address: SCTR, 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

summary: We report the transcriptional changes in mouse alveolar epithelial type 2 cells (AEC2) 7 days following tamoxifen induced expression of a clinical surfactant protein c mutation (C185G). Mouse AEC2 from SP-C wild type and uninduced SP-C C185Gneo mice were used as controls.

overall_design: Transciptional changes in isolated alveolar epithelial type 2 cells following SP-C mutation expression were compared to SP-C WT and hypomorphic (SP-C C185Gneo) control samples 7 days following induced gene expression

first: Katzen

last: Jeremy

first: Beers

last: Michael

first: Babu

last: Apoorva


title: Intersection of Regulatory Pathways Controlling Hemostasis and Hemochorial Placentation [rat II]

status: Public on Nov 25 2021

city: Kansas City

first: Khursheed

last: Iqbal

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

summary: Tissue factor pathway inhibitor (TFPI) is a prominent regulator of blood coagulation and an intriguing constituent of trophoblast cells situated at the maternal-fetal interface. The actions of TFPI extend beyond controlling hemostasis and directly affect trophoblast cell development. TFPI facilitates the differentiation of rat and human trophoblast stem cells into the invasive trophoblast/extravillous cell lineage and promotes intrauterine trophoblast invasion and trophoblast-guided uterine spiral artery remodeling at the maternal-fetal interface. Thus, TFPI is a conserved regulator of a fundamental event determining the efficacy of the hemochorial placenta.

overall_design: Tfpi was knocked down in rat trophoblast stem cells using lentiviral delivery of shRNA. Following selection by puromycin, cells were differentiated for eight days. On day eight of differentiation, cells treated with either control shRNA or Tfpi-specific shRNA were collected and RNA was isolated.

first: Masanaga

last: Muto

first: Michael

last: Soares


title: 4-1BB overexpression in basal keratinocytes induces the disruption of the eye's immune privilege

city: Muenster

first: Karin

last: Loser

state: NRW

address: von-Esmarch-Strasse 58

department: Dermatology Experimental Dermatology and Immunobiology of the Skin

institute: University of Muenster

summary: Analysis of whole transcript in mice with overexpression of 4-1BB under the control of keratin 14 promoter. The study analyze the whole transcript from all eye tissue obtained from C57/BL6 (WT control), K14-4-1BB (355) low copy number mice, K14-4-1BB (389) full blown disease mice (uveitis and cataract) and K14-4-1BB (389) onset of disease mice (eye inflammation).

overall_design: Total eye tissue analyzed obtained  from mice of different genetic strain: WT (C57/BL6); K14-4-1BB (355); K14-4-1BB (389) full blown disease; K14-4-1BB (389) onset of disease

first: E

last: Gonnelli

first: M

last: Kasper

first: V

last: Kupas

first: D

last: Bauer

first: A

last: Heiligenhaus

first: K


title: Single cell analysis of kidneys in model of DNA damage

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

summary: The effect on murine kidneys in a model of Cockayne Syndrome

overall_design: Either WT, Adh5 KO, Csb KO or a double KO were given methanol as a DNA damaging agent prior to harvest. Whole kidneys were taken for single cell using the 10x platform

first: Lee

last: Mulderrig

first: Zewen

middle: K

last: Tuong

first: Menna

last: latworthy

first: Ketan

last: Patel


title: Differentially expressed genes induced by TPA  stimulation between the P2ry6+/+ and P2ry6-/- mice

city: shanghai

first: peng

last: xu

address: Yanchang Road 301，shanghai

institute: shanghai tenth  people’s  hospital

summary: We report that P2ry6-deficient mice exhibit marked resistance to 7,12-dimethylbenzanthracene (DMBA)/12-O-tetradecanoylphorbol-13-acetate (TPA)-induced two-stage skin papilloma formation compared with wild-type mice. Consistent with these findings, epidermal hyperplasia in response to TPA stimulation was suppressed in the P2ry6 knockout or MRS2578 (P2RY6 antagonist)-treated mice. The dramatic decrease in hyperplasia and tumorigenesis due to P2ry6 disruption was associated with the suppression of TPA-induced keratinocyte proliferation and inflammatory reactions.We have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish differentially expressed genes induced by TPA stimulation between the P2ry6+/+ and P2ry6-/- mice.   Notably, P2ry6 deletion prevented the TPA-induced increase in YAP nuclear accumulation and hence its downstream gene expression in an MST/LATS1-dependent manner.

overall_design: For the long-term two-stage carcinogenesis model, a single dose of 195 nmol of 7,12-dimethylbenz[a]anthracene (DMBA) with very high purity (> 99.8%) (Sigma, St. Louis, MO,USA) in 200 μL of acetone was applied to the shaved dorsal skin of P2ry6+/+ (n=12) and P2ry6-/- (n=12) mice. A week later, 16 nmol of TPA (Sigma) with very high purity (> 99.5%) in 200 mL of acetone was applied twice a week to the shaved back skin until the 22nd week. The tumors on the backs of the mice were counted weekly after becoming visible. The incidence of mouse tumors and multiplicity of tumors were also calculated.We took the skin tumors of P2RY6 +/+ mice and P2RY6-/- mice, and checked the differential genes through RNA extraction and gene chip technology .

first: Peng

last: Xu

first: Xiyun

last: Ye


title: Chromatin and transcriptional mechanisms regulated by TFIIS N-terminal domains (TNDs) and TND-interacting motifs (TIMs)

first: H. Courtney

last: Hodges


title: Influence of IWS1 TND-interacting motifs (TIMs) on chromatin localization patterns [ChIP-seq]

summary: To reveal the influence of TND-interacting motifs (TIMs), which bind TFIIS N-terminal domains (TNDs), we prepared KELLY cells expressing either wild-type IWS1-FLAG or IWS1-FLAG containing disruptive mutations in the unstructured TIM3 region. Following lentiviral transduction of either WT or M3 IWS1-FLAG, we performed ChIP using anti-FLAG antibodies from these samples and performed chromatin occupancy profiling using ChIP-seq. Analysis of locations reveal that both WT and M3 samples are highly enriched in at transcribed gene bodies.

overall_design: Anti-FLAG ChIP-seq in KELLY cells expressing wild-type (WT) or mutant (M3) IWS1-FLAG via lentiviral transduction.

first: Katerina

last: Cermakova

first: Vaclav

last: Veverka

first: H

middle: C


title: ciHMX overexpression in Ciona intestinalis embryos

city: Aigaleo Athens

first: Vasileios

last: Papadogiannis

address: Solonos 2

department: Zoology

country: Greece

institute: University of Oxford

summary: We recently showed HMX is expressed in bipolar tail neurons (BTN) in early embryos of Ciona intestinalis. In order to assess the function of the homeobox transcription factor in this cell fate, we used an overexpression strategy. ciHMX was overexpressed in the epidermis, followed by RNAseq of experimental and control embryos. We then looked for differential expression of BTN fate markers, testing if HMX is able to regulate BTN fate determination.

overall_design: The full ciHMX ORF was inserted in a reporter construct, under the control of the epiB promoter, which drives expression in the epidermis. An epiB::YFP reporter construct was also used as a control. After in vitro fertilization and dechorionation, we then electroporated parallel batches with either epiB::YFP only (control) or epiB::YFP and epiB::Hmx (Hmx overexpression) constructs. Embryos were grown to the tailbud stage when YFP was visible, identifying transgenic embryos which were then manually selected and processed for RNA extraction. Three full biological replicates were performed on embryo batches derived from different fertilizations, with each biological replicate combining RNA from at least 50 individual embryos. All six RNA samples were sequenced by Illumina HiSeq4000 following polyA selection, yielding approximately 28 million paired end 75bp reads per sample.

first: Sebastian

last: Shimeld


title: Expression data in bone marrow mesenchymal stromal cells derived from acute myeloid leukemia patients

first: Jingying

last: Cheng

state: State...

address: 288 Nanjing Road, Heping District, Tianjin

institute: Institute of Hematology and Blood Diseases Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College

summary:
Acute myeloid leukemia (AML) is a heterogeneous clonal disorder of hematopoietic stem/progenitor cells characterized by excessive proliferation and subsequent accumulation of immature myeloid blasts, leading to impaired hematopoiesis in the bone marrow (BM). The progression of AML is closely linked to the crosstalk between leukemic cells and the BM microenvironment, in particular the mesenchymal stromal cells (MSCs).
We compared the mRNA expression profile of BM-MSCs from newly diagnosed AML patients (n=3), relapsed AML patients (n=3) and healthy donor controls (n=3)

overall_design: BM-MSCs from both AML patients and healthy donors were isolated from bone marrow aspirates and hybridized on an Affymetrix Primeview Array

first: Tianxiang

last: Pang

first: Yajing

last: Jiang

first: Ying

last: Li


title: Intersection of Regulatory Pathways Controlling Hemostasis and Hemochorial Placentation [human]

first: Khursheed

last: Iqbal

state: Kansas

department: Pathology

overall_design: 1) Tfpi was knocked down in human trophoblast stem cells using lentiviral delivery of shRNA. Following selection by puromycin, cells were differentiated for eight days (Okae et al.) into extravillous trophoblast (EVT). On day eight of differentiation, cells treated with either control shRNA or Tfp1-specific shRNA were collected and RNA was isolated.

first: Masanaga

last: Muto

first: Michael

last: Soares


title: Remote immune processes revealed by immune-derived circulating cell-free DNA

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

summary: Blood cell counts often fail to report on immune processes occurring in remote tissues. Here we use 25 immune cell type-specific methylation patterns in circulating cell-free DNA (cfDNA) for studying 26 human immune cell dynamics. We characterized cfDNA released from specific immune cell types in 27 healthy individuals (N=242), cross sectionally and longitudinally. Immune cfDNA levels had no 28 individual steady state as opposed to blood cell counts, suggesting that cfDNA concentration reflects 29 adjustment of cell survival to maintain homeostatic cell numbers. We also observed selective elevation 30 of immune-derived cfDNA upon perturbations of immune homeostasis. Following influenza 31 vaccination (N=92), B-cell-derived cfDNA levels increased prior to elevated B-cell counts and 32 predicted efficacy of antibody production. Patients with Eosinophilic Esophagitis (N=21) and B-cell 33 lymphoma (N=27) showed selective elevation of eosinophil and B-cell cfDNA respectively, which 34 were undetectable by cell counts in blood. Immune-derived cfDNA provides a novel biomarker for 35 monitoring immune responses to physiological and pathological processes that are not accessible using 36 conventional methods.

overall_design:
To further examine the relative presence of immune cfDNA in plasma and whole blood, we employed an independent set of samples and an independent technology to measure and interpret methylation markers. We performed deconvolution of methylomes obtained by whole genome bisulfite sequencing (85x coverage), on genomic DNA from whole blood, and matched plasma cfDNA from 23 healthy donors.
*** Raw data is unavailable due to patient privacy concerns ***

first: Ilana

last: Fox-Fisher

first: Sheina

last: Piyanzin

first: Bracha-Lea

last: Ochana

first: Agnes

last: Klochendler

first: Judith

last: Magenheim

first: Ayelet

last: Peretz

first: Netanel

last: Loyfer

first: Joshua

last: Moss

first: Daniel

last: Cohen

first: Yaron

last: Drori

first: Nehemya

last: Friedman

first: Michal

last: Mandelboim

first: Marc

middle: E

last: Rothenberg

first: Julie

last: Caldwell

first: Mark

last: Rochman

first: Arash

last: Jamshidi

first: Gordon

last: Cann

first: David

last: Lavi

first: Benjamin

last: Glaser

first: Ruth

last: Shemer

first: Yuval

last: Dor


title: The conservation and divergence of epigenitic reprogramming during mammalian early development

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

institute: Tsinghua University

type: Genome variation profiling by high throughput sequencing

summary: To explore how parental epigenetic information is transmitted to the next generation across mammals, we systematically investigated the epigenomes of oocytes and early embryos among human, bovine, porcine, rat, and mouse. This unprecedented dataset revealed strikingly diverse, species-specific innovation of epigenetic transition. In oocytes, DNA methylation is restricted to active gene bodies in rodents, allowing methylation of maternal imprints but not intergenic paternal imprints. Strikingly, hypermethylation also occurs in non-transcribed regions in porcine and bovine, where paternal imprints instead reside in hypomethylated, megabase-long “CpG continents (CGCs)”. Despite the presence of H3K4me3 and H3K27me3 domains in non-human oocytes, only rodent H3K27me3 survives beyond genome activation, supporting H3K27me3-mediated imprinting. Coincidently, regulatory elements are segregated away from H3K27me3 domains, the ectopic invasion of which leads to aberrant embryonic transcription. Finally, human does not fully resemble any of the rest species. Hence, mammals invent diverse epigenetic inheritance and reprogramming which center around a delicate balance in establishing imprints while protecting other regulatory regions.

sample_organism:
Sus scrofa
Bos taurus
Mus musculus
Rattus norvegicus

overall_design: DNA methylomes, H3K4me3, H3K27me3, H3K36me2, H3K36me3 are profiled and analyzed in the gametes and preimplantation embryos among five mammalian species, including human, bovine, porcine, rat and mouse.

first: Xukun

last: Lu

first: Yu

last: Zhang


title: Intersection of Regulatory Pathways Controlling Hemostasis and Hemochorial Placentation [rat I]

first: Khursheed

last: Iqbal

overall_design: Rat trophoblast stem cells were differentiated for eight days (Okae et al.) into extravillous trophoblast (EVT). On day eight of differentiation, cells were collected and RNA was isolated.

first: Masanaga

last: Muto

first: Michael

last: Soares


title: An HIV protein mediates immune evasion by targeting cGAS–STING signaling

city: Shanghai

first: Gui

last: Qian

address: Dongan road

department: School of Basic Medical Sciences

institute: Fudan university

summary: The cyclic GMP-AMP synthase (cGAS) recognizes Y-form cDNA of HIV-1 and initiate the antiviral immune response through cGAS–STING–TBK1–IRF3–type I IFN (IFN-I) signaling cascade. HIV-1 uses several strategies to interfere with the host immune molecules and mediate immune evasion. However, the potential role of HIV-1 proteins in cGAS–STING signaling remains unclear. Here we report that the HIV-1 protein p6 suppresses HIV-1-stimulated expression of IFN-I and promotes the immune evasion. Mechanistically, p6 bound with STING and inhibited the activation of STING and the interaction between STING and TBK1. Moreover, the glutamylation of p6 at Glu6 residue inhibited the interaction between STING and TRIM32 or AMFR, which subsequently suppressed the K27- and K63-linked polyubiquitination of STING at Lys337, therefore inhibited STING activation and type I IFN production, while the mutation of Glu6 residue lost the inhibitory effect. However, CoCl2, an agonist for cytosolic carboxypeptidases (CCPs), counteracted the glutamylation of Glu6 residue of p6 and promoted IFN-I production to block the immune evasion of HIV-1. These findings not only reveal a previously unknown mechanism through which an HIV-1 protein mediate immune evasion, but also provide a new therapeutic drug candidate to treat HIV-1 infection.

overall_design: Monocyte-derived macrophages infected with WT HIV-1 or HIV-1 p6 E6A for 48h before they were lysed with RNAiso Plus according to the manufacturers' instructions. The lysates were sent to Personalbio for cDNA library construction and sequencing by Illumina NovaSeq 6000.

first: Dapeng

last: Yan


title: Difference in gene expression signatures for progenies of lenalidomide-treated megakaryocyte/erythrocyte progenitors

city: Fukuoka

first: Taro

last: Tochigi

address: Maidashi

institute: Kyushu university

summary: To clarigy the molecular mechanism underlying the IMiD-induced megakaryocytic lineage commitment in human megakaryocyte/erythrocyte progenitors, we performed transcriptome analysis of CD41-CD105+ and CD41+CD105- cells obtained from megakaryocyte/erythrocyte progenitors treated with lenalidomide for 72 hours. Differentially expressed genes were comprehensively evaluated by gene set enrichment analysis. CD105-CD41+ cells showed the enrichment in the expression of genes related to megakaryocytes and platelet, whereas genes related to erythroid lineage were negatively enriched. CD41+CD105- cells expressed higher levels of transcription factors required for megakaryocyte differentiation including FLI1, RUNX1, and MEIS1. Furthermore, we performed a knockdown strategy with small interfering RNA against MEIS1 mRNA, confirming that lenalidomide-induced megakaryocyte commitment should be due to the up-regulation of MEIS1 in megakaryocyte/erythrocyte progenitors.

overall_design: Difference in gene expression profile of CD105+ progenies and CD41+ progenies derived from lenalidomide-treated human megakaryocyte/erythrocyte progenitors were evaluated. Progenies were generated from megakayrocyte/erythrocyte progenitors of 4 individual healthy volunteers by 72-hour incubation with 10 µM lenalidomide.

first: Toshihiro

last: Miyamoto

first: Kiwamu

last: Hatakeyama

last: Kochi

first: Teppei

last: Sakoda

first: Takahiro

last: Shima

first: Goichi

last: Yoshimoto

first: Yasuo

last: Mori

first: Koji

last: Kato

last: Maeda

first: Koichi

last: Akashi

first: Yoshikane

last: Kikushige


title: Gene expression in mouse hippocampus in response to long-term calorie restriction

city: Madison

first: Jamie

last: Barger

state: WI

address: 510 Charmany Drive, Suite 263

institute: LifeGen Technologies, LLC

summary:
The effect of a long-term calorie restricted diet was evaluated in hippocampus of male mice
The dietary intervention was initiated at 14 months of age and continued until 30 months of age

overall_design: Tissues were collected from mice at 30 months of age; there were 10 microarrays used in total: gene expression was measured in 5 control-fed mice and 5 calorie restricted mice (one individual mouse per microarray)

middle: L


title: Gene expression in gastrocnemius muscle in response to calorie restriction in wildtype and Sirt3 knockout mice

summary:
The effect of calorie restriction from two to 12 months of age was evaluated in gastrocnemius muscle in both wildtype mice as well as Sirt3 knockout mice
The dietary intervention was initiated at 2 months of age and continued until 12 months of age

overall_design: Tissues were collected from mice at 12 months of age; there were 15 microarrays used in total: gene expression was measured in 3 control-fed wildtype, 4 calorie restricted wildtype mice, 4 control-fed Sirt3 knockout mice, and 4 calorie restricted Sirt3 knockout mice (one individual mouse per microarray)


title: Differential expression profile of 4T1 Breast Cancer Mouse Model

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

summary: This study aimed to investigate the protective mechanisms of DMDD liposome on breast cancer, BALB/c mice were transplanted subcutaneously with 4T1 cells into the right axilla for 1 weeks, followed by various medicines for 2 weeks. The transcriptomic analysis was performed in liver tissues by RNA-seq.

overall_design: the BALB/c mice were randomly divided into several groups: the model group and DMDD liposome-treated groups were administered, followed by various agents.

first: Xiaolin

last: Zhang

first: Xiuli

last: Liu

first: Luhui

last: Qin

first: Huo

last: Lu


title: Gene expression in rhesus monkey peripheral blood mononuclear cells (PBMCs) in response to long-term calorie restriction

summary:
The effect of a long-term calorie restricted diet was evaluated in PBMCs of rhesus monkeys
For biopsy collection, the animals were given buprenorphine (0.01-0.03 mg/kg, IM) in the morning immediately preceding all biopsies and again that afternoon

overall_design: At the time of blood collection, control animals (24-27 years old) and CR animals (24-30 years old) had been subjected to CR for 16 years


title: YciR, a specific 3′-phosphodiesterases, plays a role in the pathogenesis of Uropathogenic Escherichia coli CFT073

status: Public on Nov 24 2021

city: Tian Jin

first: Zhang

last: Sissy

address: FuKang Road

institute: Nankai university

summary: Uropathogenic Escherichia coli are a prevailing causation of urinary tract infections infections and characterized by recurrence and resistance to antibiotics due to their misuse, causing a large economic burden to individuals and countries. An early determinant of the pathogenicity of UPEC is its ability to form intracellular bacterial communities in the cytoplasm of bladder epithelial cells after its invasion for evading immune response. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a recently high frequency discussed small molecule from bacterial to trigger the innate immune response form the host while YciR has been demonstrated that had an ability to degrade the level of c-di-GMP. There is no definite conclusion in the contribution of YciR and the level of c-di-GMP in the pathogenesis of UPEC. In this study, we used transcriptomic techniques approach to analyze the gene expression profiles of UPEC at the stage of bacterial survival in bladder epithelial cells and we screened yciR gene that may be associated with virulence that was upregulated in the transcriptome by differential gene analysis. In the absence of yciR, there is a Phosphorylation of NF-kappaB analyzed by Western Blot which results in decreased bacterial colonization in vitro and a reducing in mice bladder. In this study, we identified for the first time that YciR as a virulence factor in the pathogenesis of UPEC and discovered that UPEC manipulate YciR to facilitate colonization in vitro and vivo causing acute bladder infection. In addition, we also found that hupB regulated the expression of yciR to mediate the Phosphorylation of NF-kappaB These findings further increase the understanding of the pathogenesis of UPEC and provide a theoretical basis for further studies.

overall_design: mRNA profiles of WT CFT073 in cells and LB medium

last: Si

first: Yin

last: Zhiqiu

first: Du

last: Yuhui


title: Single-cell sequencing in decidual tissues

city: Changsha

first: Lei

last: Dai

state: Hunan

address: 87 Xiangya Road

institute: Xiangya Hospital, Central South University

summary: Single-cell RNA and VDJ sequencing was performed in decidual tissues of six pregnant women before and after delivery.

overall_design: mRNA and TCR/BCR profiles in decidual tissues of six pregnant women.

first: Jingrui

last: Huang

first: Weishe


title: Gene analysis of tumor cells from mice with the Treg-specific deletion of Blimp1 compared to WT mice (NanoString Immune)

city: Birmingham

first: Jianmei

middle: Wu

last: Leavenworth

state: AL

address: 1600 6th Ave South

department: Neurosurgery, Microbiology

institute: University of Alabama at Birmingham

summary:
We observed that mice with the Treg-specific deletion of Blimp1 had delayed and smaller tumor growth associated with the activation of tumor-infiltrating immune effector cells.
To determine what extent disruptions of Treg suppressive activity by a specific deletion of Blimp1 could impact on the tumor, we assessed the gene expression of sorted tumor cells by NanoString analysis.

overall_design: Prdm1fl/flFoxP3YFP-Cre (KO) and FoxP3YFP-Cre (WT) mice were subcutaneously inoculated with B16.OVA at day 0, and intraperitoneally immunized with NP-OVA in CFA at day 0 and NP-OVA in IFA at day 7. When the tumor reached ≤ 1.5 cm3, CD45-live tumor cells were FACS-sorted from the tumors of these mice. RNA was prepared and analyzed using NanoString PanCancer Immune Profiling Panel.

middle: W


title: Ribosome profiling in DDX3X degron cell lines and complementation with sex-linked paralogs

city: San Francisco

first: Srivats

last: Venkataramanan

state: California

address: 513 Parnassus Ave, HSW 740

department: Cell and Tissue Biology

institute: University of California, San Francisco

summary: We describe the subset of transcripts that require DDX3 for efficient translation and identify similarities and differences between X- and Y- linked paralogs of DDX3.

overall_design: Ribosome profiling upon auxin-induced degradation of DDX3X, and covered with either DDX3X or DDX3Y was performed from HCT116 cells.

first: Margaret

last: Gadek

first: Lorenzo

last: Calviello

first: Kevin

last: Wilkins

first: Stephen

last: Floor


title: ABHD5 inhibits YAP-induced c-Met overexpression and colon cancer cell stemness via suppressing YAP methylation

city: Chongqing

first: juan

last: Ou

address: gaotanyan

institute: Army Medical University

summary:
Cancer stemness represents a major source of development and progression of colorectal cancer (CRC). c-Met critically contributes to CRC stemness, but how c-Met is activated in CRC remains elusive. We previously identified the lipolytic factor ABHD5 as an important tumour suppressor gene in CRC. Here, we show that loss of ABHD5 promotes c-Met activation to sustain CRC stemness in a non-canonical manner. Mechanistically, we demonstrate that ABHD5 interacts in the cytoplasm with the core subunit of the SET1A methyltransferase complex, DPY30, thereby inhibiting the nuclear translocation of DPY30 and activity of SET1A. In the absence of ABHD5, DPY30 translocates to the nucleus and supports SET1A-mediated methylation of YAP and histone H3, which sequesters YAP in the nucleus and increases chromatin accessibility to synergistically promote YAP-induced transcription of c-Met, thus promoting the stemness of CRC cells. This study reveals a novel role of ABHD5 in regulating histone/non-histone methylation and CRC stemness.
We used microarrays to detail the gene expression of HCT116 colon cancer cell  and  ABHD5 knockdown HCT116 cell.

overall_design: 6 samples were analyzed,3 for control and 3 for ABHD5 knock down

first: Yan

last: Gu

first: Yanrong

last: Chen

first: Lai

last: Wei

first: Shuang

last: Wu

first: Kaicheng

last: Shen

first: Chengxiang

last: Dong

first: Yang

last: Zhao

first: Yue

first: Chi

first: Wenling

last: Zheng

first: Jiangyi

last: He

first: Yunlong

last: Wang

first: Yifei

last: Li

first: Xiaoxin

first: Hongwei

first: Jun

last: Tan

first: Liting

first: Qi

last: Zhou

first: Ganfeng

last: Xie

first: Houjie

last: Liang

first: Juanjuan


title: Oxidative damage and delayed replication allow viable Mycobacterium tuberculosis to go undetected [TnSeq]

city: New York

first: Kohta

last: Saito

state: NY

address: 413 E 69th St

institute: Weill Cornell Medicine

summary: “Viable but non-culturable” (VBNC) states pose challenges for environmental and clinical microbiology, but their biological mechanisms remain obscure. Mycobacterium tuberculosis (Mtb), the leading cause of death from infection until COVID-19, affords a striking example. Mtb can enter into a “differentially detectable” (DD) state associated with phenotypic antimicrobial resistance in which Mtb cells are viable but undetectable as colony-forming units. We found that Mtb cells enter the DD state when they undergo sublethal oxidative stress that damages their DNA, proteins, and lipids, and in addition, their replication is delayed, allowing repair. Mycobacterium bovis and BCG fail to enter the DD state under similar conditions. These findings have implications for TB latency, detection, relapse, treatment monitoring, and development of regimens that overcome phenotypic antimicrobial resistance.

overall_design: H37Rv Transposon-library Sequencing of outgrowth cultures after exposure to the following conditions: growth in nutrient rich media; two weeks of nutrient starvation in PBS with tyloxapol; two weeks of nutrient starvation in PBS with tyloxapol followed by 5 days of 1% DMSO exposure; two weeks of nutrient starvation in PBS with tyloxapol followed by 5 days of exposure to 100 uM rifampin. For each listed condition, the subsequent outgrowth of the transposon library was carried out on nutrient rich solid agarose media, 5 mL of nutrient rich liquid media, or 50 mL of nutrient rich liquid media. 2 experiments with 1 sample for each condition/outgrowth in each experiment.

first: Saito

last: Kohta

first: Mishra

last: Saurabh

first: Warrier

last: Thulasi

first: Mi

last: Jianjie

first: Weber

last: Elaina

first: Cicchetti

last: Nico

first: Nathan

last: Carl

first: Bean

last: Jamie


title: Oxidative damage and delayed replication allow viable Mycobacterium tuberculosis to go undetected

summary: "Viable but non-culturable” (VBNC) states pose challenges for environmental and clinical microbiology, but their biological mechanisms remain obscure. Mycobacterium tuberculosis (Mtb), the leading cause of death from infection until COVID-19, affords a striking example. Mtb can enter into a “differentially detectable” (DD) state associated with phenotypic antimicrobial resistance in which Mtb cells are viable but undetectable as colony-forming units. We found that Mtb cells enter the DD state when they undergo sublethal oxidative stress that damages their DNA, proteins, and lipids, and in addition, their replication is delayed, allowing repair. Mycobacterium bovis and BCG fail to enter the DD state under similar conditions. These findings have implications for TB latency, detection, relapse, treatment monitoring, and development of regimens that overcome phenotypic antimicrobial resistance.

overall_design: RNAseq profiles of H37Rv Mtb incubated in PBS with tyloxapol for 2 weeks, then exposed to either 1% DMSO, 10 uM rifampin, or 100 uM rifampin for 5 days. 2 separate experiments with triplicate biological replicates in each experiment.

first: Saurabh

last: Mishra

first: Thulasi

last: Warrier

first: Jianjie

last: Mi

first: Elaina

last: Weber

first: Nico

last: Cicchetti

first: Carl

last: Nathan

first: Jamie

last: Bean


title: Oxidative damage and delayed replication allow viable Mycobacterium tuberculosis to go undetected II

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design: RNAseq profiles of Mycobacterium bovis incubated in PBS with tyloxapol for 2 weeks, then exposed to either 1% DMSO, 10 uM rifampin, or 100 uM rifampin for 5 days.


title: Gene expression in mouse kidney in response to long-term calorie restriction

last: Barger

summary:
The effect of a long-term calorie restricted diet was evaluated in kidney of male mice
The dietary intervention was initiated at 14 months of age and continued until 30 months of age


title: Gene expression in mouse liver in response to krill powder

summary:
The effect of krill powder, a mixed source of protein and n-3 PUFAs from Antarctic Krill (Euphausia superba), on hepatic gene expression was analyzed in CBA/J mice. Mice were fed a low-fat control diet or a 3% (w/w) krill powder low-fat diet for three months. Gene expression profiling on liver samples revealed that the krill powder supplemented diet modulated a large number of pathways compared to the control diet, and we focused on the genes involved in metabolic processes.
Pathways involved β-oxidation, glucose metabolism, and amino acid catabolism were downregulated. In contrast, genes involved in the mitochondrial electron transport chain were upregulated. Thus, a krill powder supplemented diet had potent and specific effects on energy metabolism and oxidative phosphorylation at the gene level. This indicates that krill powder supplementation could be an approach to prevent age-related decline in mitochondrial respiratory chain function and weight loss.

overall_design: Tissues were collected from mice at five months of age (three months of consuming control or test diets); Fourteen microarrays total: two treatments x seven arrays per treatment (one individual mouse per microarray)


title: Expression data from the Neural Stem Cells (NSCs) of LPS induced depression mice model treated with Luteolin

city: Tsukuba

first: Mariem

last: Achour

state: Ibaraki

address: 1-1-1 Tennodai

institute: Alliance for Research on the Mediterranean and North Africa

summary:
Gene expression profiling reveals a potential role of Luteolin in LPS induced depression model
LPS depression induced mice were orally treated with luteolin (10 mg/kg body weight) once per day during 8 consecutive days. Microarray gene expression was conducted for isolated mice Neural Stem Cells (NSCs) . Two mice brain were used for each expermient.  The Microarray gene expression was conducted on NSCs and hipocampus from LPS depression induced depression mice (LPS group), LPS depression induced depression mice treated with luteolin(LPS+L group), Normal mice (PBS group) and Normal mice treated with luteolin (PBS+L).

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). One hundred  ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Mouse genome array strips (MG-430) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.

last: ACHOUR


title: Expression data from the hippocampus of LPS induced depression  mice model treated with Luteolin

summary:
Gene expression profiling reveals a potential role of Luteolin in LPS induced depression model
LPS depression induced mice were orally treated with luteolin (10 mg/kg body weight) once per day during 8 consecutive days. Microarray gene expression was conducted on mice hippocampal tissues. Two mice brains were used for each expermient .  The Microarray gene expression was conducted on hipocampus from LPS depression induced mice model(LPS group), LPS depression induced mice model treated with luteolin(LPS+L group), Normal mice (PBS group) and Normal mice treated with luteolin (PBS+L).


title: Transcriptome analysis of synthetic miR-124 sponge oligo and Salmonella-treated pig PBMCs

city: Jingzhou

first: Min

last: Yao

address: Jingmi Road #266

institute: Yangtze University

summary: High-density gene expression profile for synthetic miR-124 sponge oligo-treated pig PBMCs using RNA deep sequencing technology.

overall_design: Peripheral blood samples were collected from 20 healthy crossbreed (Duroc × Landrace × Yorkshire) piglets obtained from a commercial swine farm in Jingzhou, China either treated with Salmonella Typhi along or with miR-124 sponge + Salmonella Typhi without sacrificing the animals (ten males and ten females, four weeks old). At 12 h post treatment, cells were collected and total RNA was isolated. Sequencing libraries were prepared with an Illumina Truseq RNA sample preparation kit according to the manufacturer’s protocol (Illumina, San Diego, CA, USA). Single-read sequencing (read length: 50 bp) was conducted on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA).

first: Tinghua

last: Huang


title: Transcriptome profiling AZIN1 knockdown in the PC3 cell line

city: Leuven

first: Thomas

last: Van den Broeck

state: Outside U.S./Canada

address: Herestraat, 49

country: Belgium

institute: KU Leuven

summary: To identify AZIN1 induced transcriptional changes associated with cancer cell migration, RNA-sequencing of PC3 cells after AZIN1 knockdown was performed. Differential gene expression analysis resulted in 1460 differentially expressed genes.

overall_design: RNA Sequencing of siAZIN1 versus siScr (3 biological replicates) in PC3 cells/

first: Lisa

last: Moris

first: Frank

last: Claessens


title: Slc39a2-mediated Zinc Homeostasis Modulates Innate Immune Signaling in Phenylephrine-induced Cardiomyocyte Hypertrophy

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

summary: Zinc dyshomeostasis has been involved in the pathogenesis of cardiac hypertrophy; however, the dynamic regulation of intracellular zinc and its downstream signaling in cardiac hypertrophy remain largely unknown. Here we screened ZIP (SLC39) family members that were responsible for zinc uptake in a phenylephrine (PE)-induced cardiomyocyte hypertrophy model. We found that Slc39a2 was the only member that was altered at mRNA level by PE treatment in neonatal rat ventricular myocytes (NRVMs), but its protein level was not affected. Zincpyr1 staining showed a significant decrease in zinc uptake after PE treatment or after Slc39a2 knockdown in NRVMs, indicating an inhibition of its transport activity during hypertrophy. Slc39a2 deficiency caused spontaneous hypertrophy in NRVMs, and further exacerbated the hypertrophic responses after PE treatment. RNA sequencing analysis confirmed a largely aggravated pro-hypertrophic transcriptome reprogramming after Slc39a2 knockdown. Interestingly, the innate immune pathways, including NOD signaling, TOLL-like receptor, NFB, and IRFs, were substantially enriched after Slc39a2 knockdown. Whereas IRF7, the most sensitive among all IRFs, did not mediate the effect of Slc39a2 in hypertrophy, pro-hypertrophy phosphorylations of NFB and STAT3 were significantly enhanced after Slc39a2 knockdown, in parallel with degradation of IkBα protein. Our data demonstrate that SLC39A2-mediated zinc homeostasis contributes to the remodeling of innate immune signaling in cardiomyocyte hypertrophy, and provide novel insights into the pathogenesis of heart failure and its treatment.

overall_design: NRVMs were first transfected with siSlc39a2 or siNeg, then treated with PE for 36h after 12h of transfection. NRVMs were used to extracted RNA according to the manufacturer's instructions. Transcriptome sequencing of RNA was completed by Beijing Genomics Institution (BGI). Three independent biological replicate samples were sequenced for each group.

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